The Long Noncoding RNA Landscape in Amygdala Tissues from Schizophrenia PatientsResearch in Context
To date, most transcriptome studies of schizophrenia focus on the analysis of protein-coding genes. Long noncoding RNAs (lncRNAs) are emerging as key tissue-specific regulators of cellular and disease processes. The amygdala brain region has been implicated in the pathophysiology of schizophrenia. W...
| Main Authors: | , , , , , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
Elsevier
2018-08-01
|
| Series: | EBioMedicine |
| Online Access: | http://www.sciencedirect.com/science/article/pii/S2352396418302652 |
| _version_ | 1828173459543293952 |
|---|---|
| author | Tian Tian Zhi Wei Xiao Chang Yichuan Liu Raquel E. Gur Patrick M.A. Sleiman Hakon Hakonarson |
| author_facet | Tian Tian Zhi Wei Xiao Chang Yichuan Liu Raquel E. Gur Patrick M.A. Sleiman Hakon Hakonarson |
| author_sort | Tian Tian |
| collection | DOAJ |
| description | To date, most transcriptome studies of schizophrenia focus on the analysis of protein-coding genes. Long noncoding RNAs (lncRNAs) are emerging as key tissue-specific regulators of cellular and disease processes. The amygdala brain region has been implicated in the pathophysiology of schizophrenia. We performed unbiased whole transcriptome profiling of amygdala tissues from 22 schizophrenia patients and 24 non-psychiatric controls using RNA-seq. We reconstructed amygdala transcriptome and employed systems biology approaches to annotating the functional roles of lncRNAs. As a result, we identified 839 novel lncRNAs in amygdala. We found in amygdala lncRNAs are more subtype-specific than protein-coding genes. We identified functional modules associated with “synaptic transmission”, “ribosome”, and “immune responses” which were related to schizophrenia pathophysiology that involved lncRNAs. Integrative functional analyses associating individual lncRNAs with specific pathways and functions further show that amygdala lncRNAs are connected with all of these pathways. Our study presents the first systematic landscape of lncRNAs in amygdala tissue from schizophrenia cases. Keywords: Schizophrenia, Next-generation sequencing, Transcriptome, Systems biology |
| first_indexed | 2024-04-12T03:56:21Z |
| format | Article |
| id | doaj.art-990f3ca24d334f3686abcfe6a8e3ef4b |
| institution | Directory Open Access Journal |
| issn | 2352-3964 |
| language | English |
| last_indexed | 2024-04-12T03:56:21Z |
| publishDate | 2018-08-01 |
| publisher | Elsevier |
| record_format | Article |
| series | EBioMedicine |
| spelling | doaj.art-990f3ca24d334f3686abcfe6a8e3ef4b2022-12-22T03:48:49ZengElsevierEBioMedicine2352-39642018-08-0134171181The Long Noncoding RNA Landscape in Amygdala Tissues from Schizophrenia PatientsResearch in ContextTian Tian0Zhi Wei1Xiao Chang2Yichuan Liu3Raquel E. Gur4Patrick M.A. Sleiman5Hakon Hakonarson6Department of Computer Science, New Jersey Institute of Technology, Newark, New Jersey, USADepartment of Computer Science, New Jersey Institute of Technology, Newark, New Jersey, USA; Corresponding author at: Department of Computer Science, New Jersey Institute of Technology, Newark, New Jersey 07102, USA.Center for Applied Genomics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USACenter for Applied Genomics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USANeuropsychiatry Section, Department of Psychiatry, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USACenter for Applied Genomics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA; Division of Human Genetics, Department of Pediatrics, The Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USACenter for Applied Genomics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA; Division of Human Genetics, Department of Pediatrics, The Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA; Correspondence to: Hakon Hakonarson Center for Applied Genomics, The Children's Hospital of Philadelphia, 3615 Civic Center Blvd, Abramson Building, Philadelphia, Pennsylvania 19104, USA.To date, most transcriptome studies of schizophrenia focus on the analysis of protein-coding genes. Long noncoding RNAs (lncRNAs) are emerging as key tissue-specific regulators of cellular and disease processes. The amygdala brain region has been implicated in the pathophysiology of schizophrenia. We performed unbiased whole transcriptome profiling of amygdala tissues from 22 schizophrenia patients and 24 non-psychiatric controls using RNA-seq. We reconstructed amygdala transcriptome and employed systems biology approaches to annotating the functional roles of lncRNAs. As a result, we identified 839 novel lncRNAs in amygdala. We found in amygdala lncRNAs are more subtype-specific than protein-coding genes. We identified functional modules associated with “synaptic transmission”, “ribosome”, and “immune responses” which were related to schizophrenia pathophysiology that involved lncRNAs. Integrative functional analyses associating individual lncRNAs with specific pathways and functions further show that amygdala lncRNAs are connected with all of these pathways. Our study presents the first systematic landscape of lncRNAs in amygdala tissue from schizophrenia cases. Keywords: Schizophrenia, Next-generation sequencing, Transcriptome, Systems biologyhttp://www.sciencedirect.com/science/article/pii/S2352396418302652 |
| spellingShingle | Tian Tian Zhi Wei Xiao Chang Yichuan Liu Raquel E. Gur Patrick M.A. Sleiman Hakon Hakonarson The Long Noncoding RNA Landscape in Amygdala Tissues from Schizophrenia PatientsResearch in Context EBioMedicine |
| title | The Long Noncoding RNA Landscape in Amygdala Tissues from Schizophrenia PatientsResearch in Context |
| title_full | The Long Noncoding RNA Landscape in Amygdala Tissues from Schizophrenia PatientsResearch in Context |
| title_fullStr | The Long Noncoding RNA Landscape in Amygdala Tissues from Schizophrenia PatientsResearch in Context |
| title_full_unstemmed | The Long Noncoding RNA Landscape in Amygdala Tissues from Schizophrenia PatientsResearch in Context |
| title_short | The Long Noncoding RNA Landscape in Amygdala Tissues from Schizophrenia PatientsResearch in Context |
| title_sort | long noncoding rna landscape in amygdala tissues from schizophrenia patientsresearch in context |
| url | http://www.sciencedirect.com/science/article/pii/S2352396418302652 |
| work_keys_str_mv | AT tiantian thelongnoncodingrnalandscapeinamygdalatissuesfromschizophreniapatientsresearchincontext AT zhiwei thelongnoncodingrnalandscapeinamygdalatissuesfromschizophreniapatientsresearchincontext AT xiaochang thelongnoncodingrnalandscapeinamygdalatissuesfromschizophreniapatientsresearchincontext AT yichuanliu thelongnoncodingrnalandscapeinamygdalatissuesfromschizophreniapatientsresearchincontext AT raquelegur thelongnoncodingrnalandscapeinamygdalatissuesfromschizophreniapatientsresearchincontext AT patrickmasleiman thelongnoncodingrnalandscapeinamygdalatissuesfromschizophreniapatientsresearchincontext AT hakonhakonarson thelongnoncodingrnalandscapeinamygdalatissuesfromschizophreniapatientsresearchincontext AT tiantian longnoncodingrnalandscapeinamygdalatissuesfromschizophreniapatientsresearchincontext AT zhiwei longnoncodingrnalandscapeinamygdalatissuesfromschizophreniapatientsresearchincontext AT xiaochang longnoncodingrnalandscapeinamygdalatissuesfromschizophreniapatientsresearchincontext AT yichuanliu longnoncodingrnalandscapeinamygdalatissuesfromschizophreniapatientsresearchincontext AT raquelegur longnoncodingrnalandscapeinamygdalatissuesfromschizophreniapatientsresearchincontext AT patrickmasleiman longnoncodingrnalandscapeinamygdalatissuesfromschizophreniapatientsresearchincontext AT hakonhakonarson longnoncodingrnalandscapeinamygdalatissuesfromschizophreniapatientsresearchincontext |